Table 4.

Summary of Analytical Process of aCGH Dataset and Programs Used

Task	Program	Output file	Files' content
1. List and polarize aberrations of each specimen compared to total aberrations of all specimens	CGHExtractor	CSV file listing the aberrations of each specimens in a matrix format as: 1 = deletion 2 = duplication 0 = not present	Ternary coding of aberrations in relation to complete list of aberrations in all specimens.
2. Generation of input files for parsimony programs MIX and TNT	CGHExtractor	Text files in input format of MIX and TNT.	The polarized values of aberrations. Binary for MIX, and ternary for TNT
3. Generation parsimonious cladograms	MIX and TNT	• MIX produces two files named “output” and “treefile.” • TNT saves its analysis in file that has .tnt extension (saving should be done by the user)	Cladograms, and steps used to generate them
4. Extraction list of synapomorphies of each node of cladogram	SynapExtractor	• CSV file with lists of synapomorphies of eachnode. • The program processes together the gene list in a CSV file and output file from MIX or TNT.	Lists the headers of nodes from cladogram, and below each node's number a list of its synapomorphies
5. Extraction of a list of chromosomes that have aberrations for each node	ChromExtractor	• CSV file with four headers per nodes. • The program processes together the CSV file from SynapExtractor and the original aCGH data file.	Lists the following attributes: • gene name • chromosome • specimen(s) • aberration id • amplification • deletion

Our programs, CGHExtractor, SynapExtractor, and ChromExtractor, are publicly available online for downloading at http://software.phylomics.com.